Download User manual CLC Server Command Line Tools

CHAPTER 2. BASIC USAGE
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--e <integer> The number of CLC URLs that are expected to be returned. If this is not the
number of results files that match the search string. the command will return with exit code
10. This option is designed for use in scripts where you will wish to carry out validation
steps are you proceed through the pipeline. (On the command line, you check the error
code returned by the previous command by typing echo $?.
--C <integer> Specifies the column width of the help output.
2.4
Executing workflows
It is possible to execute workflows installed on the server. Workflows are described in detail
in the user manual of of CLC Genomics Workbench and CLC Genomics Server at http:
//www.clcbio.com/usermanuals.
Executing workflows is similar to executing algorithms, and the installed workflows will be listed
when the -A is omitted. Parameters that are open for change on execution are displayed when
the workflow is specified for the -A option. Please note that the parameter names have name of
the workflow element pre-pended to make sure they are always unique.
2.5
Emptying the recycling bin for a CLC Server File Location
Each CLC Server File Location has a recycling bin, where files that users delete are put. Only
members of the administrator group, as defined on the Genomics Server, can empty the recycle
bin associated with Genomics Server file locations. This is because the recycle bin is a shared
location for any given Genomics Server file location and many sites do not want all users to be
able to access it directly, that is to be able to view things or delete other people's data.
One can avoid the need to periodically go in and manually empty recycling bins by setting up a
script that is run as a cronjob, which includes a command of the following form:
clcserver -S <serverinfo> -P <portnumber> -U <adminusername> -W <password or tok
Above, $LOCATIONNAME would be replaced byt the name of the CLC Server File Location you
wish to empty the recycling bin of.